Microbiota of the gut, milk, and cowshed environment were examined at two dairy farms managed by automatic milking systems (AMS). Feed, rumen fluid, feces, milk, bedding, water, and airborne dust were collected and the microbiota on each was assessed by Illumina MiSeq sequencing. The most abundant taxa in feed, rumen fluid, feces, bedding, and water were Lactobacillaceae, Prevotellaceae, Ruminococcaceae, Ruminococcaceae, and Lactobacillaceae, respectively, at both farms. Aerococcaceae was the most abundant taxon in milk and airborne dust microbiota at farm 1, and Staphylococcaceae and Lactobacillaceae were the most abundant taxa in milk and airborne dust microbiota at farm 2. The three most prevalent taxa (Aerococcaceae, Staphylococcaceae, and Ruminococcaceae at farm 1 and Staphylococcaceae, Lactobacillaceae, and Ruminococcaceae at farm 2) were shared between milk and airborne dust microbiota. Indeed, SourceTracker indicated that milk microbiota was related with airborne dust microbiota. Meanwhile, hierarchical clustering and canonical analysis of principal coordinates demonstrated that the milk microbiota was associated with the bedding microbiota but clearly separated from feed, rumen fluid, feces, and water microbiota. Although our findings were derived from only two case studies, the importance of cowshed management for milk quality control and mastitis prevention was emphasized at farms managed by AMS.

The aim of this study was to characterize uterine, fecal, bedding, and airborne dust microbiota from postpartum dairy cows and their environment. The cows were managed by the free-stall housing system, and samples for microbiota and serum metabolite assessment were collected during summer and winter when the cows were at one and two months postpartum. Uterine microbiota varied between seasons; the five most prevalent taxa were Enterobacteriaceae, Moraxellaceae, Ruminococcaceae, Staphylococcaceae, and Lactobacillaceae during summer, and Ruminococcaceae, Lachnospiraceae, Bacteroidaceae, Moraxellaceae, and Clostridiaceae during winter. Although Actinomycetaceae and Mycoplasmataceae were detected at high abundance in several uterine samples, the relationship between the uterine microbiota and serum metabolite concentrations was unclear. The fecal microbiota was stable regardless of the season, whereas bedding and airborne dust microbiota varied between summer and winter. With regards to uterine, bedding, and airborne dust microbiota, Enterobacteriaceae, Moraxellaceae, Staphylococcaceae, and Lactobacillaceae were more abundant during summer, and Ruminococcaceae, Lachnospiraceae, Bacteroidaceae, and Clostridiaceae were more abundant during winter. Canonical analysis of principal coordinates confirmed the relationship between uterine and cowshed microbiota. These results indicated that the uterine microbiota may vary when the microbiota in cowshed environments changes.

The diversity of lactic acid bacteria (LAB) in naturally fermented foods produced in Hue, a city in the central region of Vietnam, was examined. From local markets, a total of 25 samples of three vegetable-based fermented products, specifically dua gia (bean sprouts), dua cai (cabbage), and mang chua (bamboo shoots), and two meat-based fermented products, specifically nem chua (uncooked pork) and tre (cooked pork) were obtained. The LAB diversity was assessed by quantitative real-time polymerase chain reaction (PCR) and qualitative denaturing gradient gel electrophoresis. Lactic and acetic acid contents were greater in meat-based products than in vegetable-based products. Major LAB species found in vegetable-based products ( Lactobacillus plantarum, Lactobacillus fermentum , and Lactobacillus helveticus ) were different from those identified in meat-based products ( Pediococcus pentosaceus , Weissella cibaria , and Lactococcus lactis ). The total bacterial population was approximately 10 9−10 copies/g regardless of the food item, with the proportion of Lactobacillus spp. determined to be from 78% ( dua cai ) to 94% ( nem chua ).

The objective of this study was to investigate uterine microbiota in postpartum dairy cows and barn environment by quantitative PCR and to evaluate the correlation between the microbiota in the uterus and barn environment. The study was carried out in 2 seasons of the year: summer (June to August 2017) and winter (October 2017 to March 2018) on Holstein dairy cow farm, Okayama Livestock Research Institute, Japan. A total of 116 samples, including 68 uterine and fecal samples, were collected from 9 cows in summer and 8 cows in winter, at 1 and 2 months after calving. Additionally, 48 samples of barn environment including airborne dust, bedding, feed and water samples were collected 6 times throughout each season. The quantative PCR results showed significant differences (P < 0.05) in the uterine and fecal microbiota of dairy cows at 1 and 2 months after calving. In summer, total bacteria at 2 months postpartum were higher than those at 1 month after calving, while total bacteria were the same in winter (P > 0.05). Bacteroidetes and Firmicutes in uterus and feces between 1 and 2 months after calving were not significantly different in both summer and winter (P > 0.05). The populations of Bacteroidetes, Firmicutes, and total bacteria were found to be highest in bedding compared to those in feed, airborne dust, and water from the barn environment (P < 0.05). Bacteroidetes, Firmicutes and total bacteria in uterus were closely related with those in bedding in summer, however they had the negative correlation with the microbiota of barn environment in winter, especially with fecal microbiota.